Abi-Haidar, A., Kaur, J., Maguitman, A., Radivojac, P., Rechtsteiner, A., Verspoor, K., . . . Rocha, L. M. (2008). Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks. Genome Biology, 9
(Suppl 2), S11.

Ahn, Y.-Y., Bagrow, J. P., & Lehmann, S. (2010). Link communities reveal multiscale complexity in networks. Nature, 466
(7307), 761–764.

Albert, R., & Barabasi, A.-L. (2002). Statistical mechanics of complex networks. Reviews of Modern Physics, 74
(1), 47.

Baeza-Yates, R., Ribiero-Neto, B., & Ribeiro-Neto, B. (1999). Modern information retrieval. Harlow, England: Pearson Education.

Baniamerian, A., & Menhaj, M. (2006). Fuzzy shortest paths in fuzzy graphs. In Reusch, B., (Ed.), Computational intelligence, theory and applications, (pp. 757–764). Berlin Heidelberg: Springer.

Barabasi, A.-L., & Albert, R. (1999). Emergence of scaling in random networks. Science, 286
(5439), 509–512.

Barrat, A., Barthelemy, M., Pastor-Satorras, R., & Vespignani, A. (2004a). The architecture of complex weighted networks. Proceedings of the National Academy of Sciences USA, 101, 3747.

Barrat, A., Barthélemy, M., & Vespignani, A. (2004b). Weighted evolving networks: Coupling topology and weight dynamics. Physical Review Letters, 92, 228701.

Behzadnia, P., Zarandi, S., Berangi, R., & Baniamerian, A. (2008). On updating the shortest path in fuzzy graphs. In *International Conference on Computational Intelligence for Modelling Control Automation*, pp. 1188–1193.

Bertoluzza, C., & Doldi, V. (2004). On the distributivity between t-norms and t-conorms. Fuzzy Sets and Systems, 142, 85–104.

Boguñá, M., Papadopoulos, F., & Krioukov, D. (2010). Sustaining the Internet with hyperbolic mapping. Nature communications, 1, 62.

Börner, K., Dall'Asta, L., Ke, W., & Vespignani, A. (2005). Studying the emerging global brain: Analyzing and visualizing the impact of co-authorship teams. Complexity, 10
(4), 57–67.

Bornholdt, S., & Schuster, H. G. (2003). Handbook of graphs and networks. Weinhenm: Wiley-VCH.

Brandes, U.,& Erlebach, T. (2005). Network analysis methodological foundations. Berlin Heidelberg: Springer.

Coifman, R. R., Lafon, S., Lee, A. B., Maggioni, M., Nadler, B., Warner, F., & Zucker, S. W. (2005). Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps. Proceedings of the National Academy of Sciences of the United States of America, 102
(21), 7426–7431.

Cornelis, C., De Kesel, P., & Kerre, E. E. (2004). Shortest paths in fuzzy weighted graphs. International Journal of Intelligent Systems, 19
(11), 1051–1068.

Day, W. H., & Edelsbrunner, H. (1984). Efficient algorithms for agglomerative hierarchical clustering methods. Journal of Classification, 1
(1), 7–24.

de Goes, F., Goldenstein, S., & Velho, L. (2008). A hierarchical segmentation of articulated bodies. In *Proceedings of the Symposium on Geometry Processing*, pp. 1349–1356, Aire-la-Ville, Switzerland, Switzerland. Eurographics Association.

Dijkstra, E. W. (1959). A note on two problems in connexion with graphs. Numerische Mathematik, 1, 269–271.

Ding, C. H. Q., He, X., Peng, H., & Holbrook, S. R. (2006). Transitive closure and metric inequality of weighted graphs: detecting protein interaction modules using cliques. International Journal of Data Mining and Bioinformatics, 1
(2), 162–177.

Dombi, J. (1982). A general class of fuzzy operators, the demorgan class of fuzzy operators and fuzziness measures induced by fuzzy operators. Fuzzy Sets & Systems, 8, 149–163.

Dombi, J. (2013). On a certain class of aggregative operators. Information Sciences, 245, 313–328.

Dorogovtsev, S. N., & Mendes, J. (2003). Evolution of networks. New York: Oxford University Press.

Dubois, D., & Prade, H. (1980). Fuzzy sets and systems. New York: Academic Press.

Fronczak, A., & Fronczak, P. (2009). Biased random walks in complex networks: The role of local navigation rules. Physical Review E, 80
(1), 016107.

Galvin, F., & Shore, S. (1991). Distance functions and topologies. American Mathematical Monthly, 98, 620–623.

Ginsberg, J., Mohebbi, M. H., Patel, R. S., Brammer, L., Smolinski, M. S., & Brilliant, L. (2009). Detecting influenza epidemics using search engine query data. Nature, 457
(7232), 1012–1014.

Goh, K.-I., Kahng, B., & Kim, D. (2005). Nonlocal evolution of weighted scale-free networks. Phys Rev E Stat Nonlin Soft Matter Phys, 72, 017103.

Golbeck, J., Parsia, B., & Hendler, J. (2003). Trust networks on the semantic web. Lecture Notes in Computer Science, 2782, 238–249.

Gondran, M., & Minoux, M. (2007). Dioids and semirings: Links to fuzzy sets and other applications. Fuzzy Sets and Systems, 158
(12), 1273–1294.

Grefenstette, G. (1994). Explorations in automatic thesaurus discovery. New York: Kluwer Academic.

Han, S.-C., Gu, Y.-D., & Li, H.-X. (2007). An application of incline matrices in dynamic analysis of generalized fuzzy bidirectional associative memories. Fuzzy Sets and Systems, 158
(12), 1340–1347.

Han, S.-C. & Li, H.-X. (2004). Indices and periods of incline matrices. Linear Algebra and its Applications, 387, 143–165.

Hirschman, L., Yeh, A., Blaschke, C., & Valencia, A. (2005). Overview of biocreative: Critical assessment of information extraction for biology. BMC Bioinformatics, 6
(Suppl 1), S1.

Klamt, S., Haus, U., & Theis, F. (2009). Hypergraphs and cellular networks. PLoS Computational Biology, 5
(5), 1–6.

Klein, M. C. (1991). Fuzzy shortest paths. Fuzzy Sets and Systems, 39
(1), 27–41.

Klement, E., Mesiar, R., & Pap, E. (2004). Triangular norms. position paper ii: General constructions and parameterized families. Fuzzy Sets and Systems, 145
(3), 411–438.

Klement, E. P., Mesiar, R., & Pap, E. (2000). Triangular norms. Dordrecht, Netherlands: Kluwer Academic Publishers.

Klir, G., & Yuan, B. (1995). Fuzzy sets and fuzzy logic, theory and applications. Upper Saddle River, NJ: Prentice Hall PTR.

Kolchinsky, A., Abi-Haidar, A., Kaur, J., Hamed, A. A., & Rocha, L. M. (2010). Classification of protein-protein interaction full-text documents using text and citation network features. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7
(3), 400–411.

Krioukov, D., Papadopoulos, F., Kitsak, M., Vahdat, A., & Boguñá, M. (2010). Hyperbolic geometry of complex networks. Physical Review E, 82
(3), 036106.

Lafon, S., & Lee, A. (2006). Diffusion maps and coarse-graining: A unified framework for dimensionality reduction, graph partitioning, and data set parameterization. IEEE Transactions on Pattern Analysis and Machine Intelligence, IEEE Transactions on, 28
(9), 1393–1403.

Markines, B., Stoilova, L., & Menczer, F. (2006). Social bookmarks for collaborative search and recommendation. In *Bookmark Hierarchies an Collaborative Recommendation*. pp. 1375–1380.

Menger, K. (1942). Statistical metrics. Proceedings of the National Academy of Sciences, 28
(12), 535–537.

Miyamoto, S. (1990). Fuzzy sets in information retrieval and cluster analysis. Dordrecht, Netherlands: Kluwer Academic Publishers.

Monge, P. R., & Contractor, N. S. (2003). Theories of communication networks. Oxford: Oxford University Press.

Mordeson, J., & Nair, P. (2000). Fuzzy graphs and fuzzy hypergraphs. Heidelberg: Physica-Verlag.

Nakamura, K., Iwai, S., & Sawaragi, T. (1982). Decision support using causation knowledge base. IEEE Transactions on Systems, Man and Cybernetics, IEEE Transactions on, 12
(6), 765–777.

Newman, M. E. (2001a). Scientific collaboration networks. ii. shortest paths, weighted networks, and centrality. Physical Review E: Statistical, Nonlinear, and Soft Matter Physics, 64
(1), 016132.

Newman, M. E. (2001b). The structure of scientific collaboration networks. Proceedings of the National Academy of Sciences USA, 98
(2), 404–409.

Newman, M. E. J. (2004). Fast algorithm for detecting community structure in networks. Physical Review E, 69
(6), 066133.

Noh, J. D.,& Rieger, H. (2004). Random walks on complex networks. Physical Review Letters, 92
(11), 118701.

Nuutila, E. & Soisalon-Soininen, E. (1994). On finding the strongly connected components in a directed graph. Information Processing Letters, 49
(1), 9–14.

Oltvai, Z., & Barabasi, A. (2002). Systems biology. Life's complexity pyramid. Science, 298
(5594), 763–764.

Pang, C.-T. (2003). On the sequence of consecutive powers of fuzzy matrix with max-archimedean-t-norms. Fuzzy Sets & Systems, 138
(3), 643–656.

Pastor-Satorras, R., & Vespignani, A. (2004). Evolution and structure of the Internet a statistical physics approach. Cambridge, UK: Cambridge University Press.

Popescu, M., Keller, J., & Mitchell, J. (2006). Fuzzy measures on the gene ontology for gene product similarity. IEEE/ACM Transactions on Computational Biology and Bioinformatics, IEEE/ACM Transactions on, 3, 263–274.

Pujol, J. M., Sangüesa, R., & Delgado, J. (2002). Extracting reputation in multi agent systems by means of social network topology. In AAMAS '02: Proceedings of the 1st International Joint Conference on Autonomous Agents and Multiagent Systems, New York, NY, USA. ACM Press, pp. 467–474.

Rocha, L. M. (1999). Evidence sets: Modeling subjective categories. International Journal of General Systems, 27
(6):457–494.

Rocha, L. M. (2001). Combination of evidence in recommendation systems characterized by distance functions. In *2002 IEEE International Conference on Fuzzy Systems: FUZZ-IEEE'02; May 12–17 2002; Honolulu, HI, United States*.

Rocha, L. M. (2002a). Proximity and semi-metric analysis of social networks. Technical report, Los Alamos National Laboratory: LAUR 02-6557.

Rocha, L. M. (2002b). Semi-metric behavior in document networks and its application to recommendation systems. In Loia, V. (Ed.), Soft computing agents: a new perspective for dynamic information systems, International Series Frontiers in Artificial Intelligence and Applications, Amsterdam, Netherlands: IOS Press, pp. 137–163.

Rocha, L. M. (2003). Automatic conversation driven by uncertainty reduction and combination of evidence for recommendation agents. In NATO Advanced Research Workshop on Systematic Organisation of Information in Fuzzy Systems; October 24–26, 2001; Vila Real, PORTUGAL. IOS Press.

Rocha, L. M. & Bollen, J. (2001). Biologically motivated distributed designs for adaptive knowledge management. In Cohen, I & Segel, L. (Eds.), Design Principles for the Immune System and other Distributed Autonomous Systems, Oxford: Oxford University Press, pp. 305–334.

Rocha, L., Simas, T., Rechtsteiner, A., DiGiacomo, M., & Luce, R. (2005). Mylibrary@lanl: Proximity and semi-metric networks for a collaborative and recommender web service. In I. Press (Ed.) *Proceedings of the 2005 IEEE/WIC/ACM International Conference on Web Intelligence (WI'05)*, pp. 565–571.

Rubinov, M., & Sporns, O. (2010). Complex network measures of brain connectivity: Uses and interpretations. Neuroimage, 52
(3), 1059–69.

Serrano, M. A., Boguna, M., & Sagues, F. (2012). Uncovering the hidden geometry behind metabolic networks. Molecular BioSystems, 8
(3), 843–850.

Serrano, M. A., Krioukov, D. & Boguñá, M. (2008). Self-similarity of complex networks and hidden metric spaces. Physical Review Letters, 100
(7), 078701.

Shenoi, S., & Melton, A. (1989). Proximity relations in the fuzzy relational database model. Fuzzy Sets and Systems, 31
(3), 285–296.

Siek, J., Lee, L.-Q., & Lumsdaine, A. (2002). The boost graph library. Boston, MA: Addison-Wesley.

Simas, T., & Rocha, L. M. (2012). Semi-metric networks for recommender systems. In *2012 IEEE/WIC/ACM International Conferences on Web Intelligence and Intelligent Agent Technology*, Macau, pp. 175–179.

Stadler, B. M., Stadler, P. F., Wagner, G. P., & Fontana, W. (2001). The topology of the possible: Formal spaces underlying patterns of evolutionary change. Journal of Theoretical Biology, 213
(2), 241–274.

Stoilova, L., Holloway, T., Markines, B., Maguitman, A. G., & Menczer, F. (2005). Givealink: Mining a semantic network of bookmarks for web search and recommendation. In LinkKDD '05: Proceedings of the 3rd International Workshop on Link discovery, New York, NY, USA. ACM, pp. 66–73.

Strehl, A. (2002). *Relationship-based Clustering and Cluster Ensembles for High-dimensional Data Mining*. PhD thesis, Austin University of Texas.

Turney, P. D. (2001). Mining the Web for synonyms: PMI–IR versus LSA on TOEFL. *Lecture Notes in Computer Science, Proceedings of the Twelfth European Conference on Machine Learning (ECML-2001)*. Freiburg, Germany, 491–502, NRC 44893.

Verspoor, K., Cohn, J., Joslyn, C., Mniszewski, S., Rechtsteiner, A., Rocha, L., & Simas, T. (2005). Protein annotation as term categorization in the gene ontology using word proximity networks. BMC Bioinformatics, pages 6
(Suppl 1), S20. doi:10.1186/1471-2105-6-S1-S20.

Wall, M. E., Rechtsteiner, A., & Rocha, L. M. (2003). Singular value decomposition and principal component analysis. In Berrar, D., Dubitzky, W., & Granzow, M., (Eds.) A practical approach to microarray data analysis, pp. 91–109. Norwell, MA: Kluwer.

Wang, W.-X., Wang, B.-H., Hu, B., Yan, G., & Ou, Q. (2005). General dynamics of topology and traffic on weighted technological networks. Physical Review Letters, 94
(18), 188702.

Wasserman, S., & Faust, K. (1994). Social networks analysis: Methods and applications. Cambridge: Cambridge University Press.

Watts, D. J., & Strogatz, S. H. (1998). Collective dynamics of ‘small-world’ networks. Nature(London), 393
(6684), 440–442.

Yan, G., Zhou, T., Wang, J., Fu, Z.-Q., & Wang, B.-H. (2005). Epidemic spread in weighted scale-free networks. Chinese Physics Letters, 22
(2), 510.

Ying, M. (1994). A logic for approximate reasoning. Journal of Symbolic Logic, 59
(3), 830–837.

Zadeh, L. (1965). Fuzzy sets and systems. In Fox, J. (Ed.), System theory, pp. 29–37. Brooklyn, NY: Elsevier.

Zadeh, L. (1999). Fuzzy logic and the calculi of fuzzy rules, fuzzy graphs, and fuzzy probabilities. Computers & Mathematics with Applications, 37
(11–12), 35.

Zwick, U. (2002). All pairs shortest paths using bridging sets retangular matrix multiplication. Journal of the ACM, 49
(3), 289–317.